The first and obvious one is Turners weapon amnesia between levels in the overgrowth campaign. Picked up a sword and dagger last level. Now they're gone.

Enemies dropped a shitload of daggers in a massive ambush (the slaver ambush btw was perhaps a too radical jump in difficulty, but at least the checkpoints lets you kinda cheese it), after surviving such an ambush you and your companion decide that it's better to leave these incredibly useful weapons behind. The game could also use a system to remember weaponry during checkpoints

Another baffling thing that has been removed from the alphas I noticed is the ability to drop weapons. Why would you do such a design decision? At least let players bind it to a key. It's specially important since you don't have total control over picking up weapons.

Not sure about level transitions, but Weapon checkpoints are having something done about them. At the very least, checkpoints spawn you with the weapon Turner should be carrying at said point (namely the boat level in which by the last checkpoint you spawn with both a sword and a knife).

You can still drop weapons, it's just been modified so you don't accidentally drop them or throw them when you don't want to. Now to drop them you have to crouch, look down and press Q.

They gotta fix some for of tutorial for dropping weapons too, because at least the Overgrowth campaign.

The game might otherwise need some sort of tutorial dojo too to help newcomers grasp the combat system. As us pre-orderers have most likely been explained the tricks and quirks of the combat system by the many development videos.